%global __brp_check_rpaths %{nil}
%global __requires_exclude ^libmpi
%global packname  VBJM
%global packver   0.1.0
%global rlibdir   /usr/local/lib/R/library

Name:             R-CRAN-%{packname}
Version:          0.1.0
Release:          1%{?dist}%{?buildtag}
Summary:          Variational Inference for Joint Model

License:          GPL-2
URL:              https://cran.r-project.org/package=%{packname}
Source0:          %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz


BuildRequires:    R-devel >= 3.6.0
Requires:         R-core >= 3.6.0
BuildRequires:    R-CRAN-survival >= 3.2
BuildRequires:    R-CRAN-pracma >= 2.2
BuildRequires:    R-CRAN-statmod >= 1.4
BuildRequires:    R-CRAN-Matrix >= 1.3
BuildRequires:    R-CRAN-Rcpp >= 1.0.0
BuildRequires:    R-CRAN-RcppArmadillo 
BuildRequires:    R-CRAN-RcppEnsmallen 
Requires:         R-CRAN-survival >= 3.2
Requires:         R-CRAN-pracma >= 2.2
Requires:         R-CRAN-statmod >= 1.4
Requires:         R-CRAN-Matrix >= 1.3
Requires:         R-CRAN-Rcpp >= 1.0.0

%description
The shared random effects joint model is one of the most widely used
approaches to study the associations between longitudinal biomarkers and a
survival outcome and make dynamic risk predictions using the
longitudinally measured biomarkers. One major limitation of joint models
is that they could be computationally expensive for complex models where
the number of the shared random effects is large. This package can be used
to fit complex multivariate joint models using our newly developed
algorithm Jieqi Tu and Jiehuan Sun (2023) <doi:10.1002/sim.9619>, which is
based on Gaussian variational approximate inference and is computationally
efficient.

%prep
%setup -q -c -n %{packname}

# fix end of executable files
find -type f -executable -exec grep -Iq . {} \; -exec sed -i -e '$a\' {} \;
# prevent binary stripping
[ -d %{packname}/src ] && find %{packname}/src -type f -exec \
  sed -i 's@/usr/bin/strip@/usr/bin/true@g' {} \; || true
[ -d %{packname}/src ] && find %{packname}/src/Make* -type f -exec \
  sed -i 's@-g0@@g' {} \; || true
# don't allow local prefix in executable scripts
find -type f -executable -exec sed -Ei 's@#!( )*/usr/local/bin@#!/usr/bin@g' {} \;

%build

%install

mkdir -p %{buildroot}%{rlibdir}
%{_bindir}/R CMD INSTALL -l %{buildroot}%{rlibdir} %{packname}
test -d %{packname}/src && (cd %{packname}/src; rm -f *.o *.so)
rm -f %{buildroot}%{rlibdir}/R.css
# remove buildroot from installed files
find %{buildroot}%{rlibdir} -type f -exec sed -i "s@%{buildroot}@@g" {} \;

%files
%{rlibdir}/%{packname}